VegVault


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P1: 👤Ondřej Mottl

IAVS, Colorado, USA

2025-08-02

🕹️Level0: The Quest

  • Mission: “Did vegetation in the Rocky Mountains maintain functional stability from the LGM to the present?”
  • Requirements:
    • Fossil pollen and modern vegetation plots
    • Functional traits (e.g. height, SLA, wood density)
    • Climate data from past and present
  • Obstacles:
    • Scattered formats, inconsistent taxonomies, climate rasters
    • Multiple tools, steep learning curves, and limited reproducibility

🔓The Shortcut

  • Imagine answering this question with just a few lines of code
  • Use {vaultkeepr} to:
    • Access vegetation, trait, and climate data simultaneously
    • Filter by time range, spatial boundaries, and taxa
    • Harmonise taxonomy and calculate community-weighted traits
  • Minimal code, maximum reproducibility

🆙LevelUp: VegVault

  • A global SQLite database integrating plot-based paleo- and neo-vegetation data
  • Links to functional traits, soil properties, and climate variables
  • Built for millennial-scale ecological analyses
  • Fully open-source and reproducible infrastructure

🗃️The Source Code

  • Data sources: Neotoma, BIEN, sPlotOpen, TRY, CHELSA, WoSIS
  • Taxonomic harmonisation via GBIF and {taxospace}
  • Abiotic data mapped to spatio-temporal grids
  • Modular, version-controlled pipelines with metadata

💎Key Innovations

  • Temporal integration of paleo and contemporary data
  • Plot-based vegetation records (not just species occurrences)
  • Sample-specific climate and soil context
  • Standardised taxonomy and harmonised trait domains

🛠️Controls

  • Access via {vaultkeepr} R package
  • SQL-free, tidyverse-compatible interface
  • Fully reproducible workflows via GitHub and Zenodo

💡Side Quests

  • Additional use cases:
    • Explore biome transitions and trait shifts
    • Test trait–environment relationships across time
    • Quantify ecological novelty and functional turnover
    • Reconstruct long-term diversity patterns
    • Investigate trait-based community assembly

🏆Summary

  • VegVault = open, robust, time-spanning vegetation research platform
  • Designed for reproducible, interdisciplinary ecological synthesis
  • Join the quest – the tools are ready, and the map is open!

📜Credits

  • Website, ORCID, GitHub, and Lab links
  • QR codes and short URLs for quick access
  • Acknowledgements to collaborators, funders, and data providers

🎯Bonus Stage

  • Optional backup slides:
    • VegVault database schema